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Metagenomic sequencing of the microbial soil community was used to assess the effect of various nitrogen fertilizer treatments in combination with constant rice straw return to the soil in the tiller layer of Northeast China's black paddy soil used for rice production. Here, we investigated changes in the composition, diversity, and structure of soil microbial communities in the soil treated with four amounts of nitrogen fertilizers (53, 93, 133, and 173 kg/ha) applied to the soil under a constant straw return of 7500 kg/ha, with a control not receiving N. The relationships between soil microbial community structure and soil physical and chemical properties were determined. The results showed that the available K content of the soil significantly (p < 0.05) increased in soil receiving the lowest N-fertilizer dose. When applied at high amounts, N-fertilizer changed the Chao1 and ACE indices of the soil microorganisms (p < 0.05), and the treatments resulted in significant differences in the β-diversity of the soil microorganisms. By NMDS analysis it was demonstrated that the treatment significantly affected the structure of the soil microbial communities. Redundancy analysis showed that the main physicochemical drivers behind these differences were total nitrogen, total potassium, ammonium nitrogen, total phosphorus, and available potassium. The soil microbial communities in the control treatment were negatively correlated with nitrate and ammonium nitrogen; the lowest N-fertilizer treatment produced positive correlations with total nitrogen, total potassium, and total phosphorus and negative correlations with ammonium nitrogen; the highest dose negatively correlated with total nitrogen, available potassium, available phosphorus, total phosphorus, and pH. This study showed that moderate N fertilizer application is an effective way to increase soil microbial diversity and improve soil quality. This experiment provides technical support for the application of the alternative fertilizer technology of straw return to the field and provides a theoretical basis for rational fertilization of paddy fields in a cold climate. [ABSTRACT FROM AUTHOR]

Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly in individuals with weakened immune systems. An aerobiological study was conducted to detect airborne fungi using metagenomics in three areas of Mexico City, each representing different degrees of urbanization, during the dry and rainy seasons of 2017. Seasonality showed a significant role in the composition of airborne fungi. Ascomycota predominated in the three areas sampled during dry and rainy seasons, with the genera Cladosporium and Penicillium presenting the highest relative abundances across seasons. The Agaromycetes showed an increase during the rainy season. Regarding the areas, the north and center sites showed similar meteorological conditions and fungal community composition patterns. According to the Shannon and Simpson indices, the south area showed a greater species diversity during the dry season. These insights into the interactions between urbanization, seasonality, and airborne microbial communities could contribute to more effective urban management, reduced health risks, and the promotion of sustainable development. [ABSTRACT FROM AUTHOR]

Existing studies have demonstrated the positive effects of nano-sized iron oxide on compost maturity, yet the impact of nano-sized iron oxide on phosphorus speciation and bacterial communities during the composting process remains unclear. In this study, pig manure and straw were used as raw materials, with biochar-supported nano-sized iron oxide (BC-Fe3O4NPs) as an additive and calcium peroxide (CaO2) as a co-agent, to conduct an aerobic composting experiment with pig manure. Four treatments were tested: CK (control), F1 (1% BC-Fe3O4NPs), F2 (5% BC-Fe3O4NPs), and F3 (5% BC-Fe3O4NPs + 5% CaO2). Key findings include the following. (1) BC-Fe3O4NPs increased compost temperatures, with F3 reaching 61℃; F1 showed optimal maturity (C/N ratio: 12.90). (2) BC-Fe3O4NPs promoted stable phosphorus forms; Residual-P proportions were higher in F1, F2, and F3 (25.81%, 51.16%, 51.68%) than CK (19.32%). (3) Bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria dominated. BC-Fe3O4NPs altered community composition, especially on day 7. Firmicutes dominated CK, F1, and F3; Proteobacteria dominated F2. At the genus level, day 7 showed Corynebacterium (CK), Clostridum (F1, F3), and Caldibacillus (F2) as predominant. (4) Pearson correlation analysis revealed shifted correlations between phosphorus forms and bacterial phyla after BC-Fe3O4NPs addition. Firmicutes positively correlated with NaOH-OP in F1 during the thermophilic phase, facilitating phosphate release and adsorption by BC-Fe3O4NPs. The significance of correlations diminished with increasing additive concentration; in F3, all phyla positively correlated with various phosphorus forms. [ABSTRACT FROM AUTHOR]

Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland; the results indicate that the three samples have different physicochemical characteristics and their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1 mutually demonstrate prominent roles in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting in that it plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance and their emphatic research value for microbial resistance issues. The results above have preliminarily proved the role of soil microbial communities as indicators predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change. [ABSTRACT FROM AUTHOR]

During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31–52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes' microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes. [ABSTRACT FROM AUTHOR]

Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications. [ABSTRACT FROM AUTHOR]

(1) Background: The unique geographical and climatic conditions of the Antarctic Peninsula contribute to distinct regional ecosystems. Microorganisms are crucial for sustaining the local ecological equilibrium. However, the variability in soil microbial community diversity across different regions of the Antarctic Peninsula remains underexplored. (2) Methods: We utilized metagenome sequencing to investigate the composition and functionality of soil microbial communities in four locations: Devil Island, King George Island, Marambio Station, and Seymour Island. (3) Results: In the KGI region, we observed increased abundance of bacteria linked to plant growth promotion and the degradation of pollutants, including PAHs. Conversely, Marambio Station exhibited a significant reduction in bacterial abundance associated with iron and sulfur oxidation/reduction. Notably, we identified 94 antibiotic resistance genes (ARGs) across 15 classes of antibiotics in Antarctic soils, with those related to aminoglycosides, β-lactamase, ribosomal RNA methyltransferase, antibiotic efflux, gene regulatory resistance, and ABC transporters showing a marked influence from anthropogenic activities. (4) Conclusions: This study carries substantial implications for the sustainable use, advancement, and conservation of microbial resources in Antarctic soils. [ABSTRACT FROM AUTHOR]

Urbanization growth has intensified the challenge of managing and treating increasing amounts of municipal solid waste (MSW). Landfills are commonly utilized for MSW disposal because of their low construction and operation costs. However, this practice produces huge volumes of landfill leachate, a highly polluting liquid rich in ammoniacal nitrogen (NH3-N), organic compounds, and various heavy metals, making it difficult to treat in conventional municipal wastewater treatment plants (WWTPs). In recent years, research has shown that microbial biofilms, developed on carriers of different materials and called "moving bed biofilm reactors" (MBBRs), may offer promising solutions for bioremediation. This study explored the biofilm development and the nitrification process of moving bed biofilms (MBBs) obtained from high ammonia-selected microbial communities. Using crystal violet staining and confocal laser-scanning microscopy, we followed the biofilm formation stages correlating nitrogen removal to metagenomic analyses. Our results indicate that MBBs unveiled a 10-fold more enhanced nitrification rate than the dispersed microbial community present in the native sludge of the Porto Sant'Elpidio (Italy) WWTP. Four bacterial families, Chitinophagaceae, Comamonadaceae, Sphingomonadaceae, and Nitrosomonadaceae, accumulate in structured biofilms and significantly contribute to the high ammonium removal rate of 80% in 24 h as estimated in leachate-containing wastewaters. [ABSTRACT FROM AUTHOR]

The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean. [ABSTRACT FROM AUTHOR]

The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region. [ABSTRACT FROM AUTHOR]

The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds' sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite. [ABSTRACT FROM AUTHOR]

(1) Background: The gut microbiota plays a crucial role in chronic immune activation associated with human immunodeficiency virus (HIV) infection, acquired immune deficiency syndrome (AIDS) pathogenesis, non-AIDS-related comorbidities, and mortality among people living with HIV (PLWH). The effects of antiretroviral therapy on the microbiome remain underexplored. This study aims to map the evidence of the impact of integrase strand transfer inhibitors (INSTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) on the gut microbiota of PLWH. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: Evidence suggests that INSTI-based regimes generally promote the restoration of alpha diversity, bringing it closer to that of seronegative controls, while beta diversity remains largely unchanged. INSTI-based therapies are suggested to be associated with improvements in microbiota composition and a tendency toward reduced inflammatory markers. In contrast, NNRTI-based treatments demonstrate limited recovery of alpha diversity and are linked to an increase in proinflammatory bacteria. (4) Conclusions: Based on the review of the current literature, it is indicated that INSTI-based antiretroviral therapy (ART) therapy facilitates better recovery of the gut microbiome. [ABSTRACT FROM AUTHOR]

Breed selection alters the coevolution of plant–microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1–Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites. [ABSTRACT FROM AUTHOR]

Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, genetic evidence supporting this mechanism remains insufficient. In this study, we identified over 55,000 oral translocation genes (OTGs) associated with colorectal cancer (CRC) and inflammatory bowel disease (IBD). These genes are primarily involved in signal transduction and cell wall biosynthesis and show consistency in their functions between IBD and CRC. Furthermore, we found that Leclercia adecarboxylata, a newly discovered opportunistic pathogen, has a significantly high abundance in the gut microbiota of colorectal cancer patients. OTGs of this pathogen were enriched in 15 metabolic pathways, including those associated with amino acid and cofactor metabolism. These findings, for the first time, provide evidence at the genetic level of the transfer of oral pathogens to the intestine and offer new insights into the understanding of the roles of oral pathogens in the development of gastrointestinal cancers. [ABSTRACT FROM AUTHOR]

Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3−-N, NO2−-N, PO43−-P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42−, and Cl−. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2−-N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle. [ABSTRACT FROM AUTHOR]

Metagenomic studies of mosquito viromes demonstrated a more diverse composition than just an exclusive composition of pathogenic arboviruses transmitted to humans. In our study, the virome of 866 female mosquitoes collected throughout 2020 at the São Paulo Zoo, located in the city of São Paulo/SP—Brazil, was obtained. Specifically, in this paper, we describe a new virus found by viral RNA extraction and next-generation MiSeq sequencing of a group of 23 specimens of Anopheles (Nys.) strodei. The complete genome with a length of 9709 nucleotides was characterized by a positive orientation and a single strand, with a single large ORF, which encodes a polyprotein of 2987 amino acids. The phylogenetic analysis showed an association with the viral family Iflaviridae and the Riboviria realm. We carried out comparisons with translated sequences of the capsid regions of other iflavirus, and the identities in relation to our sequence were below the minimum limit of 90%, indicating that possibly it is a new species of iflavirus. Our findings contribute to expanding knowledge of virome composition among mosquito species in Brazil and globally. Moreover, we provide a viral genome reference specific to this geographic region and Culicidae family of mosquitoes. This resource facilitates future in silico recognition and assembly of viral genomes within metagenomic datasets. [ABSTRACT FROM AUTHOR]

With blood stream infections (BSIs) representing a major cause of mortality and morbidity worldwide, blood cultures play a crucial role in diagnosis, but their clinical application is dampened by the long turn-around time and the detection of only culturable pathogens. In this study, we developed and validated a shotgun metagenomics next-generation sequencing (mNGS) test directly from positive blood culture fluid, allowing for the identification of fastidious or slow growing microorganisms more rapidly. The test was built based on previously validated next-generation sequencing tests, which rely on several key marker genes for bacterial and fungal identification. The new test utilizes an open-source metagenomics CZ-ID platform for the initial analysis to generate the most likely candidate species, which is then used as a reference genome for downstream, confirmatory analysis. This approach is innovative because it takes advantage of an open-source software's agnostic taxonomic calling capability while still relying on the more established and previously validated marker gene-based identification scheme, increasing the confidence in the final results. The test showed high accuracy (100%, 30/30) for both bacterial and fungal microorganisms. We further demonstrated its clinical utility especially for anaerobes and mycobacteria that are either fastidious, slow growing, or unusual. Although applicable in only limited settings, the Positive Blood Culture mNGS test provides an incremental improvement in solving the unmet clinical needs for the diagnosis of challenging BSIs.

Differentiating between Bacillus species is relevant in human medicine. Bacillus thuringiensis toxins might be effective against Strongyloides stercoralis, a nematode causing relevant human morbidity. Our first objective was to evaluate genomic and MALDI-TOF identification methods for B. thuringiensis. Our secondary objective was to evaluate a possible negative selection pressure of B. thuringiensis against S. stercoralis. PCR and Sanger were compared to MALDI-TOF on a collection of 44 B. cereus group strains. B. thuringiensis toxin genes were searched on 17 stool samples from S. stercoralis-infected and uninfected dogs. Metagenomic 16S rRNA was used for microbiome composition. The inter-rate agreement between PCR, Sanger, and MALDI-TOF was 0.631 k (p-value = 6.4 × 10−10). B. thuringiensis toxins were not found in dogs' stool. Bacteroidota and Bacillota were the major phyla in the dogs' microbiome (both represented >20% of the total bacterial community). Prevotella was underrepresented in all Strongyloides-positive dogs. However, the general composition of bacterial communities was not significantly linked with S. stercoralis infection. The genomic methods allowed accurate differentiation between B. thuringiensis and B. cereus. There was no association between B. thuringiensis and S. stercoralis infection, but further studies are needed to confirm this finding. We provide the first descriptive results about bacterial fecal composition in dogs with S. stercoralis infection. [ABSTRACT FROM AUTHOR]

Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment. Our results show that different microbial communities and community composition were the driving factors in the groundwater environment, and a diversity of antibiotic resistance genes in the groundwater environment was detected. The main source of antibiotic resistance gene host was determined by correlation tests and analyses. In this study, metagenomics was used for the first time to comprehensively analyze microbial communities in groundwater systems in the middle and lower reaches of the Yangtze River basin. The data obtained from this study serve as an invaluable resource and represent the basic metagenomic characteristics of groundwater microbial communities in the middle and lower reaches of the Yangtze River basin. These findings will be useful tools and provide a basis for future research on water microbial community and quality, greatly expanding the depth and breadth of our understanding of groundwater. [ABSTRACT FROM AUTHOR]

Fungi have always posed an unquestionable threat to heritage collections worldwide. Now, in a future of climate change, biological risk factors may have to be considered even more than before. Models and simulations to assess possible impacts a changing outdoor climate will have on indoor environments and, in turn, on biodeterioration are still underdeveloped and require a more substantial data basis. This study aimed at filling some of these knowledge gaps through a broad-based approach combining microclimatic and microbiological monitoring in four historic libraries in Austria with an uncontrolled indoor climate: Altenburg Abbey, Melk Abbey, Klosterneuburg Monastery and the Capuchin Monastery in Vienna. Data were generated from thermohygrometric sensors, cultivation-dependent air- and surface sampling and further surface dust sampling for cultivation-independent analyses. Results gave insights on the status quo of microbiological loads in the libraries and outdoor–indoor relationships. Influences of the geographic location and room-use on corresponding indoor fungal profiles were identified. Lower fungal diversities were found at the most rural site with the strongest climatic fluctuations and extreme values than in the most urban, sheltered library with a very stable climate. Further, the humidity-stabilizing potential of large collections of hygroscopic materials, such as books, was also examined. Implications for a sustainable approach to prevent future biodeterioration are discussed, supporting the long-term preservation of these valuable historic collections. [ABSTRACT FROM AUTHOR]

Levodopa is the mainstay of treatments for Parkinson's disease (PD), but large heterogeneity exists in patient response. Increasing evidence implicates bile acids (BAs) involved in the pathogenesis of PD. Furthermore, BAs have also participated in drug bioavailability. However, the impact of BAs on levodopa response (LR) has not been investigated. This study evaluated the association between fecal BAs and LR. Levodopa challenge test (LCT) was conducted in 92 PD patients to assess LR. A total of 36 fecal BAs and plasma levodopa concentrations were detected using LC-MS/MS. The difference of BAs between subgroups with bottom and top 30% LR were analyzed and fecal samples from the two groups were collected for metagenomic shotgun analysis. No fecal BAs were significantly correlated with LR, except for chenodeoxycholic acid-3-β-D-glucuronide (CDCA-3-β-glucuronide, R = −0.228, p-value = 0.039). We found no significant difference in BAs between subgroups with bottom and top 30% LR. What is more, no significant changes in bacterial species composition related to bile acids metabolism or in the proportional representation of genes encoding known bile acids enzymes were observed between the groups. Overall, our data do not support an association between fecal BAs and levodopa response in PD patients. More precise macro-metabolomic approaches are needed to reveal the potential association between gut microbial interactions and the treatment effect of levodopa. [ABSTRACT FROM AUTHOR]

The effective identification of bacterial and fungal isolates is essential for microbiological monitoring in environments like speleotherapeutic caves. This study compares MALDI-TOF MS and the OmniLog ID System, two high-throughput culture-based identification methods. MALDI-TOF MS identified 80.0% of bacterial isolates to the species level, while the OmniLog ID System identified 92.9%. However, species-level matches between the methods were only 48.8%, revealing considerable discrepancies. For discrepant results, MALDI-TOF MS matched molecular identification at the genus level in 90.5% of cases, while the OmniLog ID System matched only in 28.6%, demonstrating MALDI-TOF MS's superiority. The OmniLog ID System had difficulties identifying genera from the order Micrococcales. Fungal identification success with MALDI-TOF MS was 30.6% at the species level, potentially improvable with a customised spectral library, compared to the OmniLog ID System's 16.7%. Metagenomic approaches detected around 100 times more microbial taxa than culture-based methods, highlighting human-associated microorganisms, especially Staphylococcus spp. In addition to Staphylococcus spp. and Micrococcus spp. as indicators of cave anthropisation, metagenomics revealed another indicator, Cutibacterium acnes. This study advocates a multi-method approach combining MALDI-TOF MS, the OmniLog ID System, culture-based, and metagenomic analyses for comprehensive microbial identification. Metagenomic sampling on nitrocellulose filters provided superior read quality and microbial representation over liquid sampling, making it preferable for cave air sample collection. [ABSTRACT FROM AUTHOR]

Whether nitrogen (N)-metabolic versatility is a common trait of N-transforming microbes or if it only occurs in a few species is still unknown. We collected 83 soil samples from six soil types across China, retrieved 19 publicly available metagenomic marine sample data, and analyzed the functional traits of N-transforming microorganisms using metagenomic sequencing. More than 38% and 35% of N-transforming species in soil and marine ecosystems, respectively, encoded two or more N-pathways, although N-transforming species differed greatly between them. Furthermore, in both soil and marine ecosystems, more than 80% of nitrifying and N-fixing microorganisms at the species level were N-metabolic versatile. This study reveals that N-metabolic versatility is a common trait of N-transforming microbes, which could expand our understanding of the functional traits of drivers of nitrogen biogeochemistry. [ABSTRACT FROM AUTHOR]

As the amount of metagenomic sequencing continues to increase, there is a growing need for tools that help biologists make sense of the data. Specifically, researchers are often interested in the potential of a microbial community to carry out a metabolic reaction, but this analysis requires knitting together multiple software tools into a complex pipeline. Thanos offers a user-friendly R package designed for the pathway-centric analysis and visualization of the functions encoded within metagenomic samples. It allows researchers to go beyond taxonomic profiles and find out, quantitatively, which pathways are prevalent in an environment, as well as comparing different environments in terms of their functional potential. The analysis is based on the sequencing depth of the genes of interest, either in the metagenome-assembled genomes (MAGs) or in the assembled reads (contigs), using a normalization strategy that enables comparison across samples. The package can import the data from multiple formats and offers functions for the visualization of the results as bar plots of the functional profile, box plots of compare functions across samples, and annotated pathway graphs. By streamlining the analysis of the functional potential encoded in microbial communities, Thanos can enable impactful discoveries in all the fields touched by metagenomics, from human health to the environmental sciences. [ABSTRACT FROM AUTHOR]

Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of Pseudomonodota and Bacteriodota, notably the genera Flavobacterium, Aquirufa, Acidovorax, Polynucleobacter, and Limnohabitans. The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with Flavobacterium exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of Polynucleobacter and Limnohabitans. There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes erm(B), erm(F), mph(E), msr(E) (macrolides); tet(C), tet(O), tet(W), tet(Q) and tet(X) (tetracyclines); sul1 and sul2 (sulphonamides); and cfxA3, cfxA6 (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems blaOXA-58 and blaIMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring. [ABSTRACT FROM AUTHOR]

Removable denture wearers are at an increased risk of developing periodontal diseases due to biofilm deposition and microbial colonization on the denture surface. This study aimed to characterize and compare the metagenomic composition of saliva in denture wearers with different periodontal statuses. Twenty-four community-dwelling elders were recruited and grouped into denture wearers with active periodontitis (APD), non-denture wearers with active periodontitis (APXD), denture wearers with stable periodontal health conditions (SPCD), and non-denture wearers with stable periodontal health conditions (SPCXD). Saliva samples were collected and underwent Type IIB restriction-site-associated DNA for microbiome (2bRAD-M) metagenomic sequencing to characterize the species-resolved microbial composition. Alpha diversity analysis based on the Shannon index revealed no significant difference between groups. Beta diversity analysis using the Jaccard distance matrix was nearly significantly different between denture-wearing and non-denture-wearing groups (p = 0.075). Some respiratory pathogens, including Streptococcus agalactiae and Streptococcus pneumoniae, were detected as the top 30 species in saliva samples. Additionally, LEfSe analysis revealed a substantial presence of pathogenic bacteria in denture groups. In the cohort of saliva samples collected from community-dwelling elders, a remarkable abundance of certain opportunistic pathogens was detected in the microbial community. [ABSTRACT FROM AUTHOR]

In medicine, parasitic cysts (e.g., brain cysticerci) are believed to be sterile, and are primarily treated with antiparasitic medications, not antibiotics, which could prevent abscess formation and localized inflammation. This study quantified the microbial composition of parasitic cysts in a wild rodent, using multi-kingdom metagenomics to comprehensively assess if parasitic cysts are sterile, and further understand gut microbial translocation and adaptation in wildlife confined environments, outside the gut. Analysis was conducted on DNA from two hepatic parasitic cysts from a feline tapeworm, Hydatigera (Taenia) taeniaeformis, affecting a wild vole mouse (Microtus pennsylvanicus), and from feces, liver and peritoneal fluid of this and two other concurrent individual wild voles trapped during pest control in one of our university research vegetable gardens. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, Parabacteroides distasonis, Bacteroides (Bacteroidota); Klebsiella variicola, E. coli (Enterobacteriaceae); Enterococcus faecium and Lactobacillus acidophilus (Bacillota) inhabiting the cysts, and peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, and unexpectedly, a virus from the insect armyworm moth (Pseudaletia/Mythimna unipuncta), known as Mythimna unipuncta granulovirus A (MyunGV-A), in both cysts, and in one fecal and one peritoneal sample from the other non-cyst voles, indicating the survival and adaption potential of the insect virus in voles. Metagenomics also revealed a significantly lower probability of fungal detection in cysts compared to that in peritoneal fluid/feces (p < 0.05), with single taxon detection in each cyst (Malassezia and Pseudophaeomoniella oleicola). The peritoneal fluid had the highest probability for fungi. In conclusion, metagenomics revealed that bacteria/viruses/fungi coexist within parasitic cysts supporting the potential therapeutic benefits of antibiotics in cystic diseases, and in inflammatory microniches of chronic diseases, such as Crohn's disease gut wall cavitating micropathologies, from which we recently isolated similar synergistic pathogenic Bacteroidota and Enterobacteriaceae, and Bacillota. [ABSTRACT FROM AUTHOR]

University dormitories represent densely populated environments, and washing machines are potential sites for the spread of bacteria and microbes. However, the extent of antibiotic resistance gene (ARG) variation in washing machines within university dormitories and their potential health risks are largely unknown. To disclose the occurrence of ARGs and antibiotic-resistant bacteria from university dormitories, we collected samples from washing machines in 10 dormitories and used metagenomic sequencing technology to determine microbial and ARG abundance. Our results showed abundant microbial diversity, with Proteobacteria being the dominant microorganism that harbors many ARGs. The majority of the existing ARGs were associated with antibiotic target alteration and efflux, conferring multidrug resistance. We identified tnpA and IS91 as the most abundant mobile genetic elements (MGEs) in washing machines and found that Micavibrio aeruginosavorus, Aquincola tertiaricarbonis, and Mycolicibacterium iranicum had high levels of ARGs. Our study highlights the potential transmission of pathogens from washing machines to humans and the surrounding environment. Pollution in washing machines poses a severe threat to public health and demands attention. Therefore, it is crucial to explore effective methods for reducing the reproduction of multidrug resistance. [ABSTRACT FROM AUTHOR]

COVID-19, caused by SARS-CoV-2, results in respiratory and cardiopulmonary infections. There is an urgent need to understand not just the pathogenic mechanisms of this disease but also its impact on the physiology of different organs and microbiomes. Multiple studies have reported the effects of COVID-19 on the gastrointestinal microbiota, such as promoting dysbiosis (imbalances in the microbiome) following the disease's progression. Deconstructing the dynamic changes in microbiome composition that are specifically correlated with COVID-19 patients remains a challenge. Motivated by this problem, we implemented a biomarker discovery pipeline to identify candidate microbes specific to COVID-19. This involved a meta-analysis of large-scale COVID-19 metagenomic data to decipher the impact of COVID-19 on the human gut and respiratory microbiomes. Metagenomic studies of the gut and respiratory microbiomes of COVID-19 patients and of microbiomes from other respiratory diseases with symptoms similar to or overlapping with COVID-19 revealed 1169 and 131 differentially abundant microbes in the human gut and respiratory microbiomes, respectively, that uniquely associate with COVID-19. Furthermore, by utilizing machine learning models (LASSO and XGBoost), we demonstrated the power of microbial features in separating COVID-19 samples from metagenomic samples representing other respiratory diseases and controls (healthy individuals), achieving an overall accuracy of over 80%. Overall, our study provides insights into the microbiome shifts occurring in COVID-19 patients, shining a new light on the compositional changes. [ABSTRACT FROM AUTHOR]

Metagenomic sequencing of the microbial soil community was used to assess the effect of various nitrogen fertilizer treatments in combination with constant rice straw return to the soil in the tiller layer of Northeast China’s black paddy soil used for rice production. Here, we investigated changes in the composition, diversity, and structure of soil microbial communities in the soil treated with four amounts of nitrogen fertilizers (53, 93, 133, and 173 kg/ha) applied to the soil under a constant straw return of 7500 kg/ha, with a control not receiving N. The relationships between soil microbial community structure and soil physical and chemical properties were determined. The results showed that the available K content of the soil significantly (p < 0.05) increased in soil receiving the lowest N-fertilizer dose. When applied at high amounts, N-fertilizer changed the Chao1 and ACE indices of the soil microorganisms (p < 0.05), and the treatments resulted in significant differences in the β-diversity of the soil microorganisms. By NMDS analysis it was demonstrated that the treatment significantly affected the structure of the soil microbial communities. Redundancy analysis showed that the main physicochemical drivers behind these differences were total nitrogen, total potassium, ammonium nitrogen, total phosphorus, and available potassium. The soil microbial communities in the control treatment were negatively correlated with nitrate and ammonium nitrogen; the lowest N-fertilizer treatment produced positive correlations with total nitrogen, total potassium, and total phosphorus and negative correlations with ammonium nitrogen; the highest dose negatively correlated with total nitrogen, available potassium, available phosphorus, total phosphorus, and pH. This study showed that moderate N fertilizer application is an effective way to increase soil microbial diversity and improve soil quality. This experiment provides technical support for the application of the alternative fertilizer technology of straw return to the field and provides a theoretical basis for rational fertilization of paddy fields in a cold climate.

Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio’s high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing’s ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.

Existing studies have demonstrated the positive effects of nano-sized iron oxide on compost maturity, yet the impact of nano-sized iron oxide on phosphorus speciation and bacterial communities during the composting process remains unclear. In this study, pig manure and straw were used as raw materials, with biochar-supported nano-sized iron oxide (BC-Fe3O4NPs) as an additive and calcium peroxide (CaO2) as a co-agent, to conduct an aerobic composting experiment with pig manure. Four treatments were tested: CK (control), F1 (1% BC-Fe3O4NPs), F2 (5% BC-Fe3O4NPs), and F3 (5% BC-Fe3O4NPs + 5% CaO2). Key findings include the following. (1) BC-Fe3O4NPs increased compost temperatures, with F3 reaching 61℃; F1 showed optimal maturity (C/N ratio: 12.90). (2) BC-Fe3O4NPs promoted stable phosphorus forms; Residual-P proportions were higher in F1, F2, and F3 (25.81%, 51.16%, 51.68%) than CK (19.32%). (3) Bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria dominated. BC-Fe3O4NPs altered community composition, especially on day 7. Firmicutes dominated CK, F1, and F3; Proteobacteria dominated F2. At the genus level, day 7 showed Corynebacterium (CK), Clostridum (F1, F3), and Caldibacillus (F2) as predominant. (4) Pearson correlation analysis revealed shifted correlations between phosphorus forms and bacterial phyla after BC-Fe3O4NPs addition. Firmicutes positively correlated with NaOH-OP in F1 during the thermophilic phase, facilitating phosphate release and adsorption by BC-Fe3O4NPs. The significance of correlations diminished with increasing additive concentration; in F3, all phyla positively correlated with various phosphorus forms.

Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland; the results indicate that the three samples have different physicochemical characteristics and their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1 mutually demonstrate prominent roles in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting in that it plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance and their emphatic research value for microbial resistance issues. The results above have preliminarily proved the role of soil microbial communities as indicators predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change.

Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly in individuals with weakened immune systems. An aerobiological study was conducted to detect airborne fungi using metagenomics in three areas of Mexico City, each representing different degrees of urbanization, during the dry and rainy seasons of 2017. Seasonality showed a significant role in the composition of airborne fungi. Ascomycota predominated in the three areas sampled during dry and rainy seasons, with the genera Cladosporium and Penicillium presenting the highest relative abundances across seasons. The Agaromycetes showed an increase during the rainy season. Regarding the areas, the north and center sites showed similar meteorological conditions and fungal community composition patterns. According to the Shannon and Simpson indices, the south area showed a greater species diversity during the dry season. These insights into the interactions between urbanization, seasonality, and airborne microbial communities could contribute to more effective urban management, reduced health risks, and the promotion of sustainable development.

Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products' pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community. [ABSTRACT FROM AUTHOR]

Enterococcus faecium B13, selected from fermentation chili, has been proven to promote animal growth by previous studies, but it belongs to opportunistic pathogens, so a comprehensive evaluation of its probiotic properties and safety is necessary. In this study, the probiotic properties and safety of B13 were evaluated at the genetic and phenotype levels in vitro and then confirmed in vivo. The genome of B13 contains one chromosome and two plasmids. The average nucleotide identity indicated that B13 was most closely related to the fermentation-plant-derived strain. The strain does not carry the major virulence genes of the clinical E. faecium strains but contains aac(6′)-Ii, ant (6)-Ia, msrC genes. The strain had a higher tolerance to acid at pH 3.0, 4.0, and 0.3% bile salt and a 32.83% free radical DPPH clearance rate. It can adhere to Caco-2 cells and reduce the adhesion of E. coli to Caco-2 cells. The safety assessment revealed that the strain showed no hemolysis and did not exhibit gelatinase, ornithine decarboxylase, lysine decarboxylase, or tryptophanase activity. It was sensitive to twelve antibiotics but was resistant to erythromycin, rifampicin, tetracycline, doxycycline, and minocycline. Experiments in vivo have shown that B13 can be located in the ileum and colon and has no adverse effects on experiment animals. After 28 days of feeding, B13 did not remarkable change the α-diversity of the gut flora or increase the virulence genes. Our study demonstrated that E. faecium B13 may be used as a probiotic candidate. [ABSTRACT FROM AUTHOR]

Gut microbes thrive by utilising host energy and, in return, provide valuable benefits, akin to a symbiotic relationship. Here, metagenomic sequencing was performed to characterise and compare the community composition, diversity and antibiotic resistance of the gut microbiota of Relict gull (Larus relictus) and Anatidae species. Alpha diversity analysis revealed that the intestinal microbial richness of L. relictus was significantly lower than that of Anatidae, with distinct differences observed in microbial composition. Notably, the intestines of L. relictus harboured more pathogenic bacteria such as clostridium, which may contribute to the decline in their population and endangered status. A total of 117 strains of Escherichia coli were isolated, with 90.60% exhibiting full susceptibility to 21 antibiotics, while 25.3% exhibited significant biofilm formation. Comprehensive Antibiotic Resistance Database data indicated that glycopeptide resistance genes were the most prevalent type carried by migratory birds, alongside quinolone, tetracycline and lincosamide resistance genes. The abundance of resistance genes carried by migratory birds decreased over time. This metagenomic analysis provides valuable insights into the intestinal microbial composition of these wild bird species, offering important guidance for their conservation efforts, particularly for L. relictus, and contributing to our understanding of pathogen spread and antibiotic-resistant bacteria. [ABSTRACT FROM AUTHOR]

In nature, the symbiotic relationship between plants and microorganisms is crucial for ecosystem balance and plant growth. This study investigates the impact of Epichloë endophytic fungi, which are exclusively present aboveground, on the rhizosphere microbial functions of the host Melica transsilvanica. Using metagenomic methods, we analyzed the differences in microbial functional groups and functional genes in the rhizosphere soil between symbiotic (EI) and non-symbiotic (EF) plants. The results reveal that the presence of Epichloë altered the community structure of carbon and nitrogen cycling-related microbial populations in the host's rhizosphere, significantly increasing the abundance of the genes (porA, porG, IDH1) involved in the rTCA cycle of the carbon fixation pathway, as well as the abundance of nxrAB genes related to nitrification in the nitrogen-cycling pathway. Furthermore, the presence of Epichloë reduces the enrichment of virulence factors in the host rhizosphere microbiome, while significantly increasing the accumulation of resistance genes against heavy metals such as Zn, Sb, and Pb. This study provides new insights into the interactions among endophytic fungi, host plants, and rhizosphere microorganisms, and offers potential applications for utilizing endophytic fungi resources to improve plant growth and soil health. [ABSTRACT FROM AUTHOR]

Metagenomic sequencing analysis is central to investigating microbial communities in clinical and environmental studies. Short-read sequencing remains the primary approach for metagenomic research; however, long-read sequencing may offer advantages of improved metagenomic assembly and resolved taxonomic identification. To compare the relative performance for metagenomic studies, we simulated short- and long-read datasets using increasingly complex metagenomes comprising 10, 20, and 50 microbial taxa. Additionally, we used an empirical dataset of paired short- and long-read data generated from mouse fecal pellets to assess real-world performance. We compared metagenomic assembly quality, taxonomic classification, and metagenome-assembled genome (MAG) recovery rates. We show that long-read sequencing data significantly improve taxonomic classification and assembly quality. Metagenomic assemblies using simulated long reads were more complete and more contiguous with higher rates of MAG recovery. This resulted in more precise taxonomic classifications. Principal component analysis of empirical data demonstrated that sequencing technology affects compositional results as samples clustered by sequence type, not sample type. Overall, we highlight strengths of long-read metagenomic sequencing for microbiome studies, including improving the accuracy of classification and relative abundance estimates. These results will aid researchers when considering which sequencing approaches to use for metagenomic projects. [ABSTRACT FROM AUTHOR]

Microbial communities inhabiting sedimentary environments in river source regions serve as pivotal indicators of pristine river ecosystems. While the correlation between antibiotic resistome and pathogenicity with core gut bacteria in humans is well established, there exists a significant knowledge gap concerning the interaction of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) with specific microbes in river source basins, often referred to as "terrestrial gut". Understanding the microbial composition, including bacteria and resident genetic elements such as ARGs, HPB, Mobile Genetic Elements (MGEs), and Virulence Factors (VFs), within natural habitats against the backdrop of global change, is imperative. To address this gap, an enrichment-based culturomics complementary along with metagenomics was conducted in this study to characterize the microbial biobank and provide preliminary ecological insights into profiling the dissemination of ARGs in the Lancang River Source Basin. Based on our findings, in the main stream of the Lancang River Source Basin, 674 strains of bacteria, comprising 540 strains under anaerobic conditions and 124 under aerobic conditions, were successfully isolated. Among these, 98 species were identified as known species, while 4 were potential novel species. Of these 98 species, 30 were HPB relevant to human health. Additionally, bacA and bacitracin emerged as the most abundant ARGs and antibiotics in this river, respectively. Furthermore, the risk assessment of ARGs predominantly indicated the lowest risk rank (Rank Ⅳ) in terms of endangering human health. In summary, enrichment-based culturomics proved effective in isolating rare and unknown bacteria, particularly under anaerobic conditions. The emergence of ARGs showed limited correlation with MGEs, indicating minimal threats to human health within the main stream of the Lancang River Source Basin. [ABSTRACT FROM AUTHOR]

The study aims to analyze the composition of the gut microbiota in Chinese individuals using metagenomic sequencing technology, with a particular focus on the abundance of Akkermansia muciniphila (Akk). To improve the efficiency of Akk isolation and identification accuracy, modifications were made to the enrichment culture medium and 16S rRNA universal primers. Additionally, potential growth-promoting factors that stimulate Akk growth were explored through in vitro screening. The research results revealed that the abundance of Akk in Chinese fecal samples ranged from 0.004% to 0.4%. During optimization, a type of animal protein peptide significantly enhanced the enrichment efficiency of Akk, resulting in the isolation of three Akk strains from 14 fecal samples. Furthermore, 17 different growth-promoting factors were compared, and four factors, including galactose, sialic acid, lactose, and chitosan, were identified as significantly promoting Akk growth. Through orthogonal experiments, the optimal ratio of these four growth-promoting factors was determined to be 1:1:2:1. After adding 1.25% of this growth-promoting factor combination to the standard culture medium, Akk was cultivated at 37° for 36 h, achieving an OD600nm value of 1.169, thus realizing efficient proliferation and optimized cultivation of Akk. This study provides important clues for a deeper understanding of the gut microbiota composition in Chinese individuals, while also offering effective methods for the isolation and cultivation of Akk, laying the groundwork for its functional and application research in the human body. [ABSTRACT FROM AUTHOR]

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities. [ABSTRACT FROM AUTHOR]

Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient's clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols. [ABSTRACT FROM AUTHOR]

The composition of microbiota in the digestive tract gut is essential for insect physiology, homeostasis, and pathogen infection. Little is known about the interactions between microbiota load and oral infection with baculoviruses. CnmeGV is an obligative baculovirus to Cnaphalocrocis medinalis. We investigated the impact of CnmeGV infection on the structure of intestinal microbes of C. medinalis during the initial infection stage. The results revealed that the gut microbiota profiles were dynamically driven by pathogen infection of CnmeGV. The numbers of all the OTU counts were relatively higher at the early and later stages, while the microbial diversity significantly increased early but dropped sharply following the infection. The compositional abundance of domain bacteria Firmicutes developed substantially higher. The significantly enriched and depleted species can be divided into four groups at the species level. Fifteen of these species were ultimately predicted as the biomarkers of CnmeGV infection. CnmeGV infection induces significant enrichment of alterations in functional genes related to metabolism and the immune system, encompassing processes such as carbohydrate, amino acid, cofactor, and vitamin metabolism. Finally, the study may provide an in-depth analysis of the relationship between host microbiota, baculovirus infection, and pest control of C. medinalis. [ABSTRACT FROM AUTHOR]

CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications. [ABSTRACT FROM AUTHOR]

Recently, probiotics have been widely applied for the in situ remediation of aquatic water. Numerous studies have proved that probiotics can regulate water quality by improving the microbial community. Nitrogen cycling, induced by microorganisms, is a crucial process for maintaining the balance of the aquatic ecosystem. Nevertheless, the underlying mechanisms by which probiotics enhance water quality in aquatic systems remain poorly understood. To explore the water quality indicators and their correlation with nitrogen cycling-related functional genes, metagenomic analysis of element cycling was performed to identify nitrogen cycling-related functional genes in Coilia nasus aquatic water between the control group (C) and the groups supplemented with probiotics in feed (PF) or water (PW). The results showed that adding probiotics to the aquatic water could reduce the concentrations of ammonia nitrogen (NH4+-N), nitrite (NO2−-N), and total nitrogen (TN) in the water. Community structure analysis revealed that the relative abundance of Verrucomicrobiota was increased from 30 d to 120 d (2.61% to 6.35%) in the PW group, while the relative abundance of Cyanobacteria was decreased from 30 d to 120 d (5.66% to 1.77%). We constructed a nitrogen cycling pathway diagram for C. nasus aquaculture ponds. The nitrogen cycle functional analysis showed that adding probiotics to the water could increase the relative abundance of the amoC_B and hao (Nitrification pathways) and the nirS and nosZ (Denitrification pathways). Correlation analysis revealed that NH4+-N was significantly negatively correlated with Limnohabitans, Sediminibacterium, and Algoriphagus, while NO2−-N was significantly negatively correlated with Roseomonas and Rubrivivax. Our study demonstrated that adding probiotics to the water can promote nitrogen element conversion and migration, facilitate nitrogen cycling, benefit ecological environment protection, and remove nitrogen-containing compounds in aquaculture systems by altering the relative abundance of nitrogen cycling-related functional genes and microorganisms. [ABSTRACT FROM AUTHOR]

Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of vineyards from DOP Ribeiro on the soil's condition. Samples from soils under three different management systems were collected, and the main soil physicochemical properties were evaluated. A selection of 50 pesticides were investigated by liquid chromatography with tandem mass spectrometry. The bacterial and fungal microbiomes were characterized through amplicon sequencing. The results show that organic agriculture positively influences soil pH and the concentration of some nutrients compared to conventional management. Our microbiome analysis demonstrated that transitioning from conventional to organic management significantly improves several BeCrop® indexes related to key microbial metabolism and soil bio-sustainability. Such a transition does not affect soil alpha diversity, but leads to a higher interconnected microbial network structure. Moreover, differential core genera and species for each management system are observed. In addition, the correlation of the microbiome with geographical distance is evidence of the existence of different microbial terroirs within DOP Ribeiro. Indeed, sustainable management leads to higher nutrient availability and enhances soil health in the short term, while lowering pesticide usage. [ABSTRACT FROM AUTHOR]

Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats. [ABSTRACT FROM AUTHOR]

Porcine sapovirus (PoSaV) is one of the most significant pathogens causing piglet diarrhea, and one with limited genetic characterization. In this study, the prevalence, infection pattern, and genetic evolution of porcine sapovirus were elucidated in detail. The positive rate of PoSaV was 10.1% (20/198), with dual, triple, and quadruple infections of 45%, 40%, and 5%, respectively. To further explore the viral composition in the PoSaV-positive diarrhea feces, metagenomic sequencing was carried out. The results confirmed that RNA viruses accounted for a higher proportion (55.47%), including the two primary viruses of PoSaV (21.78%) and porcine astrovirus (PAstV) (24.54%) in the tested diarrhea feces samples. Afterward, a full-length sequence of the PoSaV isolate was amplified and named SHCM/Mega2023, and also given the identifier of GenBank No. PP388958. Phylogenetic analysis identified the prevalent PoSaV strain SHCM/Mega2023 in the GIII genogroup, involving a recombinant event with MK962338 and KT922089, with the breakpoint at 2969–5132 nucleotides (nt). The time tree revealed that the GIII genogroup exhibits the widest divergence time span, indicating a high likelihood of viral recombination. Moreover, SHCM/Mega2023 had three nucleotide "RPL" insertions at the 151–153 nt site in the VP2 gene, compared to the other GIII strains. Further selective pressure calculations demonstrate that the whole genome of the SHCM/Mega2023 strain was under purifying selection (dN/dS < 1), with seven positively selected sites in the VP1 protein, which might be related to antigenicity. In conclusion, this study presents a novel genomic evolution of PoSaV, offering valuable insights into antigenicity and for vaccine research. [ABSTRACT FROM AUTHOR]

Astragalus is a medicinal plant with obvious rhizosphere effects. At present, there are many Astragalus plants with high application value but low recognition and resource reserves in the northwestern area of Yunnan province, China. In this study, metagenomics was used to analyze the microbial diversity and community structure of rhizosphere soil of A. forrestii, A. acaulis, and A. ernestii plants grown in a special high-cold environment of northwestern Yunnan, China, at different altitudes ranging from 3225 to 4353 m. These microbes were taxonomically annotated to obtain 24 phyla and 501 genera for A. forrestii, 30 phyla and 504 genera for A. acaulis, as well as 39 phyla and 533 genera for A. ernestii. Overall, the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Acidobacteria, while the dominant fungal ones were Ascomycota and Basidiomycota. At the genus level, Bradyrhizobium, Afipia, and Paraburkholderia were the most prevalent bacteria, and Hyaloscypha, Pseudogymnoascus, and Russula were the dominant fungal genera. Some of them are considered biocontrol microbes that could sustain the growth and health of host Astragalus plants. Redundancy analysis revealed that pH, TN, and SOM had a significant impact on the microbial community structures (p < 0.05). Finally, triterpene, flavonoid, polysaccharide, and amino acid metabolisms accounted for a high proportion of the enriched KEGG pathways, which possibly contributed to the synthesis of bioactive constituents in the Astragalus plants. [ABSTRACT FROM AUTHOR]